Autofire is, what the NPRs use. It does not work very good for player races, messing up all your settings (as you have noticed allready).
It will, for example, re-allocate all your PD weapons to offensive tasks, re-assign missile launchers as the AI sees fit (usually, in a way you would not) and similar stuff.
General consensus is: Don´t use it!
Note: As far as I have been able to determine the NPR design all have only one single type of weapon on a ship (i.e. a DDG will only mount ASM launchers, never any PD turret or AMM launchers) plus some CIWS. Autofire _might_ work, if you design your ships in a similar way.